Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome

ABSTRACT: Here we employed a non-enzymatic chemical labeling approach to introduce lactylation on lysine residues of model peptides and proteins. Tandem MS acquisition of lactylated peptide carriers on different MS platforms unequivocally led us to note an intense peak corresponding to the “cyclic” immonium ion of lactyllysine that is generated from the “linear” immonium ion upon the loss of NH3. The cycIm ion provides superior sensitivity and specificity as a lactylation marker than the linIm ion. Together, the ability to confidently identify protein lactylation empowers mapping the landscape of human lactylation proteome and fosters ensuing investigation into the regulatory mechanisms of lactylation when our understanding to this newly discovered PTM is still during its infancy.

ORGANISM(S): Homo Sapiens

SUBMITTER: Hui Ye

PROVIDER: PXD028488 | iProX | Wed Sep 15 00:00:00 BST 2021

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome.

Wan Ning N Wang Nian N Yu Siqin S Zhang Hanqing H Tang Shuo S Wang Dexiang D Lu Wenjie W Li Huanhuan H Delafield Daniel G DG Kong Ying Y Wang Xinmiao X Shao Chang C Lv Langlang L Wang Guangji G Tan Renxiang R Wang Nanxi N Hao Haiping H Ye Hui H

Nature methods 20220627 7

Lactylation was initially discovered on human histones. Given its nascence, its occurrence on nonhistone proteins and downstream functional consequences remain elusive. Here we report a cyclic immonium ion of lactyllysine formed during tandem mass spectrometry that enables confident protein lactylation assignment. We validated the sensitivity and specificity of this ion for lactylation through affinity-enriched lactylproteome analysis and large-scale informatic assessment of nonlactylated spectr ...[more]

PMID: 35761067

Similar Datasets

Cyclic ion mobility for hydrogen/deuterium exchange-mass spectrometry applications

Project description:Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localisation of dynamic changes. Consequently, HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase data quality by providing an orthogonal mode of peptide ion separation in the gas-phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage and/or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multi-pass IM separations. Using 1-pass and multi-pass cIM routines, we use the recently commercialised SELECT SERIES™ Cyclic™ IM spectrometer for HDX-MS analyses of 4 detergent solubilised IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multi-pass cIM data. Interestingly, use of 1-pass and multi-pass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM which has the potential to enable the analysis of more complex systems with greater accuracy and speed.

2024-04-08 | PXD048293 | Pride

Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. To make cDNA libraries, we exploited the 2’, 3’-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. Using Arabidopsis thaliana tRNA ligase, RNA fragments with 2’, 3’-cyclic phosphates were covalently attached to defined RNA linkers containing an 8-base long unique molecular identifier (UMI) sequence. Libraries prepared in this manner contain cDNA derived exclusively from RNA fragments with 2', 3'-cyclic phosphates. The UMI sequence allows for detailed quantitation. We optimized and validated 2’, 3’-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A, and RNA from uninfected and poliovirus-infected HeLa cells.

2014-02-07 | E-GEOD-52489 | biostudies-arrayexpress

Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

2014-02-07 | GSE52489 | GEO

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

Project description:Background: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. Results: Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs. Conclusions: Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software.

2017-08-04 | GSE98562 | GEO

Cyclic stretch and interstial sitffness effects on A549 cells

Project description:The mechanical properties and forces in the extracellular environment surrounding alveolar epithelial cells modulate their behavior. Particularly, breathing applies 3-dimensional cyclic stretch to the cells, while diseases such as cancer or fibrosis induce stiffening of the interstitium. To model this behavior, a biomimetic device was developed that effectively imitates the active forces in the alveolus, while allowing one to control the interstitium matrix stiffnesses to recreate different mechanical environments to replicate lung diseases. Alveolar epithelial A549 cancer cells were cultured on the platforms and their transcriptome was profiled using RNA sequencing.

2024-09-30 | GSE272292 | GEO

SLC19A1 transports immunoreactive cyclic dinucleotides

Project description:SLC19A1 transports immunoreactive cyclic dinucleotides

| PRJNA554882 | ENA

A phase I/II clinical study of Carbon Ion Radiotherapy using 1 fraction for Liver Metastasis from Colorectal Cancer

Project description:Interventions: Prescribed heavy-ion beam (carbon-ion beam) dose. Initial dose 36Gy(RBE). Dose escalated until dose limiting toxicity is met. Primary outcome(s): Acute toxicity and initial tumor response Study Design: expanded access Non-randomized

| 2648031 | ecrin-mdr-crc

Gene expression profiles of four murine tumors after carbon-ion (C-ion) or gamma irradiation.

Project description:This study uses microarray analysis to examine the fate of multiple C-ion-irradiated tumors in vivo to gain a comprehensive overview of the changes in gene expression induced by C-ion irradiation. Four murine tumors were irradiated in vivo with C-ions at a single dose, and gamma-rays were used as a reference beam. Keywords: mouse squamous cell carcinoma and fibrosarcoma, carbon ion-irradiation, gamma-irradiation, resected sample, transplanted tissues

2008-06-09 | GSE11629 | GEO

Cyclic dinucleotide stimulation of Nematostella vectensis

Project description:Cyclic dinucleotide stimulation of Nematostella vectensis

| PRJNA734503 | ENA

Genome-wide analysis of mDC transcriptional response to cyclic glucan

Project description:Analysis of transcriptional profiles in mDC sorted from apheresed PBMC and stimulated for 6 hours with cyclic glucan or LPS. The hypothesis tested is that cyclic glucan induces maturation and T cell-activation transcripts in human mDC. Total RNA extracted from mDC sorted from apheresed PBMC and activated for 6 hours with cyclic glucan or LPS.

2012-12-31 | E-GEOD-32023 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data